Mendelian Randomization Analysis: Oily Fish Intake and Alzheimer's Disease

By Dr. Shea Andrews, generated on 2018-08-24

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Data sources

***[Oily Fish Intake (Canela-Xandri et al BioRxiv 2018)]: Summary statisitcs for Oily Fish Intake were determined from the UK Biobank with participatns asked How often do you eat oily fish?. Results were reported in GeneATLAS, a large database of associations between hundreds of traits and millions of variants using the UK Biobank cohort.

Late Onset Alzheimer’s disease (LOAD, Lambert et al 2013): The International Genomics of Alzheimer’s Project (IGAP) is a meta-analysis of 4 previously published GWAS datasets: the European Alzheimer’s Disease Imitative (EADI), the Alzheimer Disease Genetics Consortium (ADGC), Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE), and Genetic and Environmental Risk in AD (GERAD) and includes a sample of 17,008 LOAD cases and 37,154 cognitively normal elder controls. Participants in IGAP were of European ancestry, the average age was 71 and 58.4% of participants were women.

Alzheimer’s Age of Onset Surivial (AAOS, Huang et al 2017): A GWAS of age of onset in LOAD was conducted in 14,406 AD case samples and 25,849 control samples from the IGAP using Cox proportional hazard regressions. Participants were of European ancestry, in cases the the average AAO was 74.8 and 61.7% were women, in controls the average AAE was 79.0 and 59.6% were women.

CSF Ab42, tau & ptau (AB42, ptau, tau, Deming et al 2017): A GWAS of CSF AB42, ptau and tau levels (pg/mL) was conducted in 3,146 participants. Participants were of Eurpean ancestry.

Instrumental Vaibles

LD Clumping: For standard two sample MR it is important to ensure that the instruments for the exposure are independent. LD clumping can be performed using the data_clump function from the TwoSampleMR package, which uses EUR samples from the 1000 genomes project to estimate LD between SNPs and amonst SNPs that have and LD above a given threshold, only the SNP with the lowest p-value will be retained.

Proxy SNPs: SNPs associated with Oily Fish Intake were extracted from the GWAS of LOAD, AAOS, AB42, ptau and tau. Where SNPs were not available in the outcome GWAS, the EUR thousand genomes was queried to identified potential proxy SNPs that are in linkage disequilibrium (r2 > 0.8) of the missing SNP.

Oily Fish Intake

Oily Fish Intake: 8241 SNPs (Table 1) were assoicated with were associated with Oily Fish Intake at p < 5e-8. After LD clumping, 8107 of 8241 SNPs were removed.

Table 1: Independent SNPS associated with Oily Fish Intake

LOAD

Of the the 134 SNPs associated with Oily Fish Intake, 106 were available in the LOAD GWAS (Table 2).

Table 2: SNPS associated with Oily Fish Intake avalible in LOAD GWAS

AAOS

Of the the 134 SNPs associated with Oily Fish Intake, 115 were available in the AAOS GWAS (Table 3).

Table 3: SNPS associated with available in AAOS GWAS

AB42

Of the the 134 SNPs associated with Oily Fish Intake, 89 were available in the CSF AB42 GWAS (Table 4).

Table 4: SNPS associated with Oily Fish Intake avalible in ab42 GWAS

Ptau

Of the the 134 SNPs associated with Oily Fish Intake, 98 were available in the CSF Ptau GWAS (Table 5).

Table 5: SNPS associated with Oily Fish Intake avalible in Ptau GWAS

Tau

Of the the 134 SNPs associated with Oily Fish Intake, 89 were available in the CSF Tau GWAS (Table 6).

Table 6: SNPS associated with Oily Fish Intake avalible in tau GWAS

Data harmonization

Harmonize the exposure and outcome datasets so that the effect of a SNP on the exposure and the effect of that SNP on the outcome correspond to the same allele. The harmonise_data function from the TwoSampleMR package can be used to perform the harmonization step, by default it try’s to infer the forward strand alleles using allele frequency information. EAF were not availbe in the IGAP summary statisitics, as such the allele frequencies reported in the AAOS anaylsis were used.

Oily Fish Intake ~ LOAD

Table 7: Harmonized Oily Fish Intake and LOAD datasets

Oily Fish Intake ~ AAOS

Table 8: Harmonized Oily Fish Intake and AAOS datasets

Oily Fish Intake ~ AB42

Table 9: Harmonized Oily Fish Intake and AB42 datasets

Oily Fish Intake ~ Ptau

Table 10: Harmonized Oily Fish Intake and Ptau datasets

Oily Fish Intake ~ Tau

Table 11: Harmonized Oily Fish Intake and Tau datasets

Pleiotropy

Pleiotropy was assesed using Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO), that allows for the evlation of evaluation of horizontal pleiotropy in a standared MR model. MR-PRESSO performs a global test for detection of horizontal pleiotropy and correction of pleiotropy via outlier removal.

Oily Fish Intake ~ LOAD: The MR-PRESSO global test for pleiotropy was significant (p = <1e-04). The following SNPs were removed due to pleiotropy: rs6857

Oily Fish Intake ~ AAOS: The MR-PRESSO global test for pleiotropy was significant (p = <1e-04). The following SNPs were removed due to pleiotropy: rs6857

Oily Fish Intake ~ AB42: The MR-PRESSO global test for pleiotropy was significant (p = <1e-04).. The following SNPs were removed due to pleiotropy: rs6857

Oily Fish Intake ~ Ptau: The MR-PRESSO global test for pleiotropy was significant (p = <1e-04).. The following SNPs were removed due to pleiotropy: rs17050031, rs6857

Oily Fish Intake ~ Tau: The MR-PRESSO global test for pleiotropy was significant (p = <1e-04).. The following SNPs were removed due to pleiotropy: rs17151667, rs7013471

Mendelian Randomization Analysis

To obtain an overall estimate of causal effect, the SNP-exposure (Major Depressive Disorder) and SNP-outcome coefficients (Alzheimer’s disease and Alzheimer’s Age of Onset) were combined in 1) a random-effects meta-analysis using an inverse-variance weighted approach (IVW); 2) a Weighted Median approach; 3) and Egger Regression. IVW is equivalent to a weighted regression of the SNP-outcome coefficients on the SNP-exposure coefficients with the intercept constrained to zero. This method assumes that all variants are valid instrumental variables based on the Mendelian randomization assumptions. The causal estimate of the IVW analysis expresses the causal increase in the outcome (or log odds of the outcome for a binary outcome) per unit change in the exposure. Weighted median MR allows for 50% of the instrumental variables to be invalid. MR-Egger regression allows all the instrumental variables to be subject to direct effects (i.e. horizontal pleiotropy), with the intercept representing bias in the causal estimate due to pleiotropy and the slope representing the causal estimate.

Oily Fish Intake ~ LOAD

Figure 1 illustrates the SNP-specific associations with Oily Fish Intake versus the association between each SNP and risk of LOAD.

Fig. 1: Scatterplot of SNP effects for the association of Trait and LOAD

Figure 2 and Table 1 shows the SNP-specific effects and overall IVW, weighted median and Egger regression causal estimates of genetically predicted Oily Fish Intake on risk of LOAD.

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations

Table 1: MR estimates for Oily Fish Intake and LOAD

Figure 3 shows a funnel plot to detect pleiotropy and Table 2 show the results of Cochrans Q heterogeneity test to assess for the presence of pleiotropy.

Fig. 3: Funnel plot of the Trait – LOAD causal estimates against their precession

Table 2: Heterogenity tests for Oily Fish Intake and LOAD

## Warning in mr_heterogeneity(trait_LOAD.MRdat, method_list =
## c("mr_egger_regression", : Prior to version 0.4.9 there was a bug in
## the IVW Q statistic estimate, leading to a slight underestimation in
## heterogeneity. This has now been resolved.

Table 3: Test for directional pleitropy for Oily Fish Intake and LOAD

Oily Fish Intake ~ AAOS

Figure 4 illustrates the SNP-specific associations with Oily Fish Intake versus the association between each SNP and AAOS.

Fig. 4: Scatterplot of SNP effects for the association of Trait and AAOS

Figure 5 and Table 4 shows the SNP-specific effects and overall IVW, weighted median and Egger regression causal estimates of genetically predicted Oily Fish Intake on AAOS.

Fig. 5: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations

Table 4: MR estimates for Oily Fish Intake and AAOS

Figure 6 shows a funnel plot to detect pleiotropy and Table 5 show the results of Cochrans Q heterogeneity test to assess for the presence of pleiotropy.

Fig. 6: Funnel plot of the traitohol Conumption – AAOS causal estimates against their precession

Table 5: Heterogenity tests for Oily Fish Intake and AAOS

## Warning in mr_heterogeneity(trait_AAOS.MRdat, method_list =
## c("mr_egger_regression", : Prior to version 0.4.9 there was a bug in
## the IVW Q statistic estimate, leading to a slight underestimation in
## heterogeneity. This has now been resolved.

Table 6: Test for directional pleitropy for Oily Fish Intake and AAOS

Oily Fish Intake ~ AB42

Figure 1 illustrates the SNP-specific associations with Oily Fish Intake versus the association between each SNP and AB42.

Fig. 1: Scatterplot of SNP effects for the association of trait and AB42

Figure 2 and Table 7 shows the SNP-specific effects and overall IVW, weighted median and Egger regression causal estimates of genetically predicted Oily Fish Intake CSF AB42 levels.

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations

Table 7: MR estimates for Oily Fish Intake and AB42

Figure 3 shows a funnel plot to detect pleiotropy and Table 8 show the results of Cochrans Q heterogeneity test to assess for the presence of pleiotropy.

Fig. 3: Funnel plot of the trait – AB42 causal estimates against their precession

Table 8: Heterogenity tests for Oily Fish Intake and AB42

## Warning in mr_heterogeneity(trait_AB42.MRdat, method_list =
## c("mr_egger_regression", : Prior to version 0.4.9 there was a bug in
## the IVW Q statistic estimate, leading to a slight underestimation in
## heterogeneity. This has now been resolved.

Table 9: Test for directional pleitropy for Oily Fish Intake and AB42

Oily Fish Intake ~ Ptau

Figure 1 illustrates the SNP-specific associations with Oily Fish Intake versus the association between each SNP and risk of Ptau.

Fig. 1: Scatterplot of SNP effects for the association of trait and Ptau

Figure 2 and Table 9 shows the SNP-specific effects and overall IVW, weighted median and Egger regression causal estimates of genetically predicted Oily Fish Intake on risk of Ptau.

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations

Table 9: MR estimates for Oily Fish Intake and Ptau

Figure 3 shows a funnel plot to detect pleiotropy and Table 10 show the results of Cochrans Q heterogeneity test to assess for the presence of pleiotropy.

Fig. 3: Funnel plot of the trait – Ptau causal estimates against their precession

Table 10: Heterogenity tests for Oily Fish Intake and Ptau

## Warning in mr_heterogeneity(trait_Ptau.MRdat, method_list =
## c("mr_egger_regression", : Prior to version 0.4.9 there was a bug in
## the IVW Q statistic estimate, leading to a slight underestimation in
## heterogeneity. This has now been resolved.

Table 11: Test for directional pleitropy for Oily Fish Intake and Ptau

Oily Fish Intake ~ Tau

Figure 1 illustrates the SNP-specific associations with Oily Fish Intake versus the association between each SNP and CSF Tau levels.

Fig. 1: Scatterplot of SNP effects for the association of trait and Tau

Figure 2 and Table 12 shows the SNP-specific effects and overall IVW, weighted median and Egger regression causal estimates of genetically predicted Oily Fish Intake on risk of Tau.

Fig. 2: Forrest plot of Wald ratios and 95% CIs for SNP-specific and overall IVW, Weighted median and Egger associations

Table 12: MR estimates for Oily Fish Intake and Tau

Figure 3 shows a funnel plot to detect pleiotropy and Table 13 show the results of Cochrans Q heterogeneity test to assess for the presence of pleiotropy.

Fig. 3: Funnel plot of the trait – Tau causal estimates against their precession

Table 14: Heterogenity tests for Oily Fish Intake and Tau

## Warning in mr_heterogeneity(trait_Tau.MRdat, method_list =
## c("mr_egger_regression", : Prior to version 0.4.9 there was a bug in
## the IVW Q statistic estimate, leading to a slight underestimation in
## heterogeneity. This has now been resolved.

Table 15: Test for directional pleitropy for Oily Fish Intake and Tau

MR analysis results